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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 58);
use_ok 'Bio::SeqIO';
}
my $verbose = test_debug();
my @formats = qw(gcg fasta raw pir tab ace );
# The following files or formats are failing: swiss genbank interpro embl
for my $format (@formats) {
print "======== $format ========\n" if $verbose;
my $seq;
my $str = Bio::SeqIO->new( -file => test_input_file("test.$format"),
-format => $format );
is $str->format(), $format;
ok $seq = $str->next_seq();
print "Sequence 1 of 2 from $format stream:\n", $seq->seq, "\n\n" if $verbose;
unless ($format eq 'raw') {
is $seq->id, 'roa1_drome',"ID for format $format";
is $seq->length, 358;
}
unless ($format eq 'gcg') { # GCG file can contain only one sequence
ok $seq = $str->next_seq();
print "Sequence 2 of 2 from $format stream:\n", $seq->seq, $seq->seq, "\n" if $verbose;
}
my $outfile = test_output_file();
my $out = Bio::SeqIO->new( -file => ">$outfile",
-format => $format );
ok $out->write_seq($seq);
if ($format eq 'fasta') {
my $id_type;
ok($id_type = $out->preferred_id_type('accession.version'),
'accession.version');
}
ok -s $outfile;
}
# from testformats.pl
SKIP: {
test_skip(-tests => 6, -requires_modules => [qw(Algorithm::Diff
IO::ScalarArray
IO::String)]);
use_ok 'Algorithm::Diff';
eval "use Algorithm::Diff qw(diff LCS);";
use_ok 'IO::ScalarArray';
use_ok 'IO::String';
my %files = (
#'test.embl' => 'embl',
#'test.ace' => 'ace',
'test.fasta' => 'fasta',
#'test.game' => 'game',
'test.gcg' => 'gcg',
#'test.genbank' => 'genbank',
'test.raw' => 'raw',
#'test_badlf.gcg' => 'gcg'
);
while( my ($file, $type) = each %files ) {
my $filename = test_input_file($file);
print "processing file $filename\n" if $verbose;
open my $FILE, '<', $filename or die "Could not read file '$filename': $!\n";
my @datain = <$FILE>;
close $FILE;
my $in = IO::String->new( join('', @datain) );
my $seqin = Bio::SeqIO->new( -fh => $in,
-format => $type );
my $out = IO::String->new();
my $seqout = Bio::SeqIO->new( -fh => $out,
-format => $type );
my $seq;
while( defined($seq = $seqin->next_seq) ) {
$seqout->write_seq($seq);
}
$seqout->close();
$seqin->close();
my $strref = $out->string_ref;
my @dataout = map { $_."\n"} split(/\n/, $$strref );
my @diffs = &diff( \@datain, \@dataout);
is @diffs, 0;
if(@diffs && $verbose) {
foreach my $d ( @diffs ) {
foreach my $diff ( @$d ) {
chomp($diff->[2]);
print $diff->[0], $diff->[1], "\n>", $diff->[2], "\n";
}
}
print "in is \n", join('', @datain), "\n";
print "out is \n", join('',@dataout), "\n";
}
}
}
# simple tests specific to Bio::SeqIO interface (applicable to all SeqIO
# modules)
##############################################
# test format() and variant() in Bio::RootIO
##############################################
my $in = Bio::SeqIO->new(
-file => test_input_file('bug2901.fa'),
-format => "fasta",
);
is $in->format, 'fasta';
is $in->variant, undef;
$in = Bio::SeqIO->new(
-file => test_input_file('fastq', 'illumina_faked.fastq'),
-format => "fastq",
-variant => 'illumina',
);
is $in->format, 'fastq';
is $in->variant, 'illumina';
######################################################
# test format detection from different inputs
######################################################
$in = Bio::SeqIO->new( -file => test_input_file('test.fastq') );
is $in->format, 'fastq';
open my $fh, '<', test_input_file('test.genbank') or die "Could not read file 'test.genbank': $!\n";
$in = Bio::SeqIO->new( -fh => $fh );
is $in->format, 'genbank';
close $fh;
my $string = ">seq\nACGATCG\n";
$in = Bio::SeqIO->new( -string => $string );
is $in->format, 'fasta';
############ EXCEPTION HANDLING ############
TODO: {
local $TODO = 'file/fh-based tests should be in Bio::Root::IO, see issue #3204';
throws_ok {
Bio::SeqIO->new();
} qr/No file, fh, or string argument provided/, 'Must pass a file or file handle';
}
throws_ok {
Bio::SeqIO->new(-fh => undef);
} qr/fh argument provided, but with an undefined value/,
'Must pass a file or file handle';
throws_ok {
Bio::SeqIO->new(-file => undef);
} qr/file argument provided, but with an undefined value/,
'Must pass a file or file handle';
throws_ok {
Bio::SeqIO->new(-file => 'foo.bar');
} qr/Could not read file 'foo.bar':/,
'Must pass a real file';
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